Variant report

Variant	rs28641638
Chromosome Location	chr15:59215233-59215234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59212424..59217333-chr15:59223129..59226870,5	MCF-7	breast:
2	chr15:59205247..59208199-chr15:59214036..59216910,3	K562	blood:

Variant related genes	Relation type
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10162821	0.91[ASN][1000 genomes]
rs10518991	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10518992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1078001	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1092172	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071400	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11071401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630160	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631540	0.90[CEU][hapmap]
rs11636723	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11858989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148858	0.90[ASN][1000 genomes]
rs12438918	0.86[EUR][1000 genomes]
rs12438961	0.89[EUR][1000 genomes]
rs12440904	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12443436	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595482	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12708456	0.95[ASN][1000 genomes]
rs12909894	0.82[ASN][1000 genomes]
rs12910580	0.90[CEU][hapmap];0.84[TSI][hapmap]
rs12914723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916751	0.91[ASN][1000 genomes]
rs1446240	0.85[CEU][hapmap]
rs17302038	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17302045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs173214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013117	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2270664	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2279719	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28473013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28529423	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28538484	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28709922	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3145	0.82[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[ASN][1000 genomes]
rs35477914	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs431414	0.94[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4328375	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4774315	0.81[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4775101	0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[ASN][1000 genomes]
rs592407	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs604057	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs637918	0.81[EUR][1000 genomes]
rs677933	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67851431	0.92[ASN][1000 genomes]
rs694918	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71407077	0.92[ASN][1000 genomes]
rs7173317	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029301	0.85[CEU][hapmap]
rs8035628	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs813219	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
3	nsv904270	chr15:59140329-59238415	Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv3405065	chr15:59214360-59215508	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59168600-59220000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:59169200-59223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59170800-59224200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:59179800-59224200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:59180800-59216400	Weak transcription	Stomach Mucosa	stomach
6	chr15:59182200-59224200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:59192200-59223400	Weak transcription	Right Ventricle	heart
8	chr15:59192600-59223400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:59192800-59221200	Weak transcription	Small Intestine	intestine
10	chr15:59192800-59223200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:59192800-59224200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:59193000-59217000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:59193000-59219000	Weak transcription	Spleen	Spleen
14	chr15:59193000-59223200	Weak transcription	Aorta	Aorta
15	chr15:59193000-59223200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:59193000-59224200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:59193000-59224200	Weak transcription	Colonic Mucosa	Colon
18	chr15:59193000-59224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:59194000-59223600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:59194200-59216800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:59195600-59215600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:59197200-59225000	Weak transcription	Gastric	stomach
23	chr15:59199800-59217000	Weak transcription	Psoas Muscle	Psoas
24	chr15:59199800-59224200	Weak transcription	Esophagus	oesophagus
25	chr15:59200600-59224200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:59202000-59219000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:59202200-59219000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:59203200-59221000	Weak transcription	Brain Substantia Nigra	brain
29	chr15:59203800-59215600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:59206800-59217600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:59207000-59216200	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:59207000-59216200	Weak transcription	NHLF	lung
33	chr15:59207200-59219200	Weak transcription	Brain Germinal Matrix	brain
34	chr15:59208000-59215400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:59208000-59216200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:59208000-59217000	Weak transcription	Fetal Kidney	kidney
37	chr15:59208000-59223200	Weak transcription	Brain Angular Gyrus	brain
38	chr15:59208000-59223200	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:59209000-59217600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:59209200-59217000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:59209400-59215400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:59209400-59216400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:59209400-59219400	Weak transcription	HSMMtube	muscle
44	chr15:59209600-59216200	Weak transcription	NHDF-Ad	bronchial
45	chr15:59209600-59217400	Weak transcription	HSMM	muscle
46	chr15:59209600-59218400	Weak transcription	HMEC	breast
47	chr15:59209600-59218400	Weak transcription	NH-A	brain
48	chr15:59209600-59223400	Weak transcription	Fetal Brain Male	brain
49	chr15:59209600-59223400	Weak transcription	Fetal Brain Female	brain
50	chr15:59209800-59216800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links